That's a 1-up point. There's one in the second stage that you need the yellow/red gun to get.
And yes, some enemies are weaker to certain weapons than others, or at least that's how it works out anyway. A lot of stuff just doesn't get hurt by the blue weapon much at all for example, and the green gun rips through certain targets really fast.
There's also a weird set of enemies part way through the game (maybe stage 3?) where if you shoot them with the blue gun, they will get pulled in towards you. If you aren't expecting this it will kill you real quick, but if you do it carefully you can actually pull the enemies off the screen to avoid fighting them.
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